Electrophoresis

This week, to determine the quantity of DNA yielded from each extraction method, (QuickExtract DNA extraction kit, boiling, microwave and enzymatic digestion followed by heating) agarose electrophoresis was performed. Through this, I became very confused with the results. Before I get into this, in the first slot, I had inserted a PCR MW Ruler. After that, the following slots from 2-13 were filled with 1 microliter of dye mixed with 5 microliters of DNA from QE1 (QuickExtract protocol), QE2, QE3, M2 (microwave protocol), M3-1, M3-2, M4, B3 (boiling protocol), EDL2 (enzymatic digestion followed by heating using Ready-Lyse Lysozyme), EDL3, EDL4, EDL5 and EDP1 (enzymatic digestion followed by heating using proteinase K) respectively. Using the NanoDrop spectrophotometer (Figures 1 and 2), it is shown that the enzymatic followed by digestion samples had relatively a higher amount of DNA (looking under the column “nucleic acid”). With that said, I was expecting that slots 10 and beyond (which had the enzymatic digestion followed by heating samples) would have bright strands of DNA. The brighter the strands, the more DNA would be present. However, to my surprise, that was not the case. Instead, the microwave method, which had less DNA than mentioned protocol, had brighter strands. As a matter of fact, slots 9-14 appear to have no strands at all (Figure 3). Next week, PCR will be performed on these samples to determine if I have any DNA. In the meantime, I am hoping that the PCR will not cause any further confusion.

Figure 1. NanoDrop Spectrophotometer nucleic acid report of all samples from different DNA extraction methods.

Figure 2. NanoDrop Spectrophotometer nucleic acid report of all samples from different DNA extraction methods.

Figur,e 3. Electrophoresis results after sampling PCR MW Ruler, QE1, QE2, QE3, M2, M3-1, M3-2, M4, B3, EDL2, EDL3, EDL4, EDL5 and EDP1 in each slot respectively.